When Genomics Is Not Enough: Experimental Evidence for a Decrease in LINE-1 Activity During the Evolution of Australian Marsupials.

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  • Author(s): Gallus S;Gallus S; Lammers F; Lammers F; Nilsson MA; Nilsson MA
  • Source:
    Genome biology and evolution [Genome Biol Evol] 2016 Aug 25; Vol. 8 (8), pp. 2406-12. Date of Electronic Publication: 2016 Aug 25.
  • Publication Type:
    Letter; Research Support, Non-U.S. Gov't
  • Language:
    English
  • Additional Information
    • Source:
      Publisher: Oxford University Press Country of Publication: England NLM ID: 101509707 Publication Model: Electronic Cited Medium: Internet ISSN: 1759-6653 (Electronic) Linking ISSN: 17596653 NLM ISO Abbreviation: Genome Biol Evol Subsets: MEDLINE
    • Publication Information:
      Original Publication: Oxford, UK : Oxford University Press
    • Subject Terms:
      Evolution, Molecular* ; Phylogeny*; Long Interspersed Nucleotide Elements/*genetics ; Marsupialia/*genetics; Animals ; Australia ; Computer Simulation ; Genomics ; Mammals/genetics
    • Abstract:
      The autonomous transposable element LINE-1 is a highly abundant element that makes up between 15% and 20% of therian mammal genomes. Since their origin before the divergence of marsupials and placental mammals, LINE-1 elements have contributed actively to the genome landscape. A previous in silico screen of the Tasmanian devil genome revealed a lack of functional coding LINE-1 sequences. In this study we present the results of an in vitro analysis from a partial LINE-1 reverse transcriptase coding sequence in five marsupial species. Our experimental screen supports the in silico findings of the genome-wide degradation of LINE-1 sequences in the Tasmanian devil, and identifies a high frequency of degraded LINE-1 sequences in other Australian marsupials. The comparison between the experimentally obtained LINE-1 sequences and reference genome assemblies suggests that conclusions from in silico analyses of retrotransposition activity can be influenced by incomplete genome assemblies from short reads.
      (© The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)
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    • Contributed Indexing:
      Keywords: LINE-1; Tasmanian devil; marsupials; retrotransposition; transposable element
    • Publication Date:
      Date Created: 20160709 Date Completed: 20170614 Latest Revision: 20181113
    • Publication Date:
      20221213
    • Accession Number:
      PMC5010896
    • Accession Number:
      10.1093/gbe/evw159
    • Accession Number:
      27389686